#!/usr/bin/env cwl-runner

label: "Prepare user input"
cwlVersion: v1.0
class: Workflow
doc: Prepare user input for  NCBI-PGAP pipeline

requirements:
  - class: MultipleInputFeatureRequirement
  - class: InlineJavascriptRequirement

inputs:
  submol: 
    type: File
  fasta:
    type: File
  taxon_db:
    type: File
steps:
    yaml2json:
        label: "yaml2json"
        run: progs/yaml2json.cwl
        in: 
            input: submol
        out: [output]

    pgapx_yaml_ctl:
        label: "pgapx_yaml_ctl"
        run: progs/pgapx_yaml_ctl.cwl
        in:
            input: yaml2json/output
            input_fasta: fasta
            taxon_db: taxon_db
        out: [output_entries, output_seq_submit, output_ltp]
    file2string:
        run: progs/file2string.cwl
        in:
             input: pgapx_yaml_ctl/output_ltp
        out: [value]
    
outputs:
    output_entries:
        type: File?
        outputSource: pgapx_yaml_ctl/output_entries
    output_seq_submit:
        type: File?
        outputSource: pgapx_yaml_ctl/output_seq_submit
    locus_tag_prefix:
        type: string
        outputSource: file2string/value